Bio Phylo Bayesian Inference
GPTomics/bioSkills
Frames Bayesian phylogenetics as approximating a posterior distribution over trees conditioned on data AND priors via an MCMC that must be proven to have converged, using MrBayes, BEAST2, RevBayes…
Tools for LiP peptide and protein significance analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb.
Install Bioconductor Msstatslip
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-msstatslip --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/transcriptomics/msstatslip .claude/skills/bioconductor-msstatslip && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "bioconductor-msstatslip" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/msstatslip into .claude/skills/bioconductor-msstatslip/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-msstatslip", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/msstatslipType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-msstatslip --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/transcriptomics/msstatslip .agents/skills/bioconductor-msstatslip && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bioconductor-msstatslip" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/msstatslip into .agents/skills/bioconductor-msstatslip/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-msstatslip", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-msstatslip --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/transcriptomics/msstatslip .cursor/skills/bioconductor-msstatslip && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bioconductor-msstatslip" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/msstatslip into .cursor/skills/bioconductor-msstatslip/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-msstatslip", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/bioMate-AI/biomate-bioconductor-kb.git --path skills/transcriptomics/msstatslip--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-msstatslip --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/transcriptomics/msstatslip .gemini/skills/bioconductor-msstatslip && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "bioconductor-msstatslip" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/msstatslip into .gemini/skills/bioconductor-msstatslip/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-msstatslip", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-msstatslipInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/transcriptomics/msstatslip .github/skills/bioconductor-msstatslip && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "bioconductor-msstatslip" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/msstatslip into .github/skills/bioconductor-msstatslip/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-msstatslip", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-msstatslip --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/transcriptomics/msstatslip .opencode/skills/bioconductor-msstatslip && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bioconductor-msstatslip" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/msstatslip into .opencode/skills/bioconductor-msstatslip/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-msstatslip", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
bioconductor-msstatslip- GitHub stars
- 804
- Token cost
- ~1.1k tokens
- SKILL.md length
- 305 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Tools for LiP peptide and protein significance analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb.
- Tasks that involve Summarization
- SKILL.md covers Workflows, When to Use, When NOT to Use and Data Requirements, plus 6 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Tasks that involve Bioinformatics
What it does
Bioconductor Msstatslip is an agent skill from bioMate-AI/biomate-bioconductor-kb. Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.
Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Summarization and Bioinformatics. The repository describes itself as: BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes.
When your agent uses it
- Tasks that involve Summarization
- Tasks that involve Bioinformatics
Example prompts
- “Use the bioconductor-msstatslip skill to tool for LiP peptide and protein significance analysis. An agent skill from…”
- “/bioconductor-msstatslip”
What it can do on your machine
Read from SKILL.md and the folder at commit c9bd4d8. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are r).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
bioconductor.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Bioconductor Msstatslip loads about 1.1k tokens when it runs. Until then it costs about 65 tokens; SKILL.md has 305 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 305 words (~1,117 tokens).
“Input: Summarized LiP-MS and TrP-MS datasets (MSstatsLiP_Summarized) and a FASTA file (fasta_file). Output: Proteolytic resistance ratios and sequence-aligned barcode plots.”
- name
- bioconductor-msstatslip
- when_to_use
- Use when: MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package; MSstatsLiP Proteolytic Workflow; Differential expression analysis…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/msstatslip of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Msstatslip next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bioconductor Msstatslip this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.1k | Automated safety check: Pass | Custom licence | |
| Bio Phylo Bayesian InferenceGPTomics/bioSkills | 1.2k | 1 repos | ~6.9k | Automated safety check: Pass | MIT | |
| Variant Analysis ToolsDrugClaw/DrugClaw | 126 | — | ~722 | Automated safety check: Pass | Apache-2.0 | |
| Bio Proteomics QuantificationGPTomics/bioSkills | 1.2k | 1 repos | ~5.9k | Automated safety check: Pass | MIT | |
| Rebuttal ResponseM1n-n9/paper-lifecycle | 693 | — | ~1.9k | Automated safety check: Pass | None | |
| Daily Paper DigestGalaxy-Dawn/claude-scholar | 5.7k | — | ~1k | Automated safety check: Pass | MIT |
Similar skills
Variant Analysis Tools
DrugClaw/DrugClaw
Variant and VCF workflow guide for local SNV, indel, and structural-variant summarization, filtering, and consequence triage.
Bio Proteomics Quantification
GPTomics/bioSkills
Quantifies protein abundance from mass spectrometry using label-free (LFQ/MaxLFQ, DIA fragment-level), isobaric (TMT/iTRAQ reporter ions, MS2 vs SPS-MS3), and metabolic (SILAC) approaches, including…
Rebuttal Response
M1n-n9/paper-lifecycle
Plan, triage, and write academic rebuttals and review responses.
Daily Paper Digest
Galaxy-Dawn/claude-scholar
Finds recent arXiv and bioRxiv papers on a topic, narrows them in stages to one pick per field, and writes bilingual Chinese and English summaries.
Literature Synthesis Guide
Jinze-Lee/codex-skills-workbench
Follow the bundled literature-synthesis guide. An agent skill from Jinze-Lee/codex-skills-workbench.
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Related
Categories
Questions about Bioconductor Msstatslip
What does Bioconductor Msstatslip do?
Tools for LiP peptide and protein significance analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb. Bioconductor Msstatslip is an agent skill from bioMate-AI/biomate-bioconductor-kb. Tools for LiP peptide and protein significance analysis.
When should I use Bioconductor Msstatslip?
Bioconductor Msstatslip fits situations like: tasks that involve Summarization; tasks that involve Bioinformatics.
How do I install Bioconductor Msstatslip in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a claude-code`. Or copy the skill folder (skills/transcriptomics/msstatslip in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-msstatslip in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Msstatslip in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a codex`. Or copy the skill folder (skills/transcriptomics/msstatslip in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-msstatslip in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Msstatslip in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-msstatslip -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bioconductor-msstatslip, .gemini/skills/bioconductor-msstatslip, .github/skills/bioconductor-msstatslip and .opencode/skills/bioconductor-msstatslip in your project.
What does Bioconductor Msstatslip need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Msstatslip is instructions for the agent only.
Does Bioconductor Msstatslip access the network?
SKILL.md names 1 domain. As links in the text: bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Msstatslip safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Bioconductor Msstatslip use?
Bioconductor Msstatslip has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Bioconductor Msstatslip use?
About 1.1k tokens (SKILL.md is roughly 4.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Bioconductor Msstatslip?
Skills that share tags, products or a category with Bioconductor Msstatslip: Bio Phylo Bayesian Inference (GPTomics/bioSkills, 1.2k stars), Variant Analysis Tools (DrugClaw/DrugClaw, 126 stars), Bio Proteomics Quantification (GPTomics/bioSkills, 1.2k stars) and Rebuttal Response (M1n-n9/paper-lifecycle, 693 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Msstatslip?
bioMate-AI (a GitHub organization) maintains it in bioMate-AI/biomate-bioconductor-kb, which has 804 GitHub stars. The repository holds 112 skills in this directory. The repository was last updated on June 20, 2026.
Source: bioMate-AI/biomate-bioconductor-kb on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.